java.lang.Object
- java.lang.Thread
- - org.jmol.thread.JmolThread
  - - org.jmol.navigate.Navigator

All Implemented Interfaces:

java.lang.Runnable, JmolNavigatorInterface
```
public final class Navigator
extends JmolThread
implements JmolNavigatorInterface
```
Navigator is a user input mechanism that utilizes the keypad to drive through the model. It is created by reflection only from org.jmol.viewer.TransformManager

Nested Class Summary
- Nested classes/interfaces inherited from class java.lang.Thread
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private javajs.util.V3`	`aaStepCenter`
`private javajs.util.V3`	`axis`
`private javajs.util.P3`	`center`
`private javajs.util.P3`	`centerStart`
`private float`	`degrees`
`private float`	`degreeStep`
`private float`	`depthDelta`
`private float`	`depthPercent`
`private float`	`depthStart`
`private float`	`floatSecondsTotal`
`private int`	`frameTimeMillis`
`private int`	`iList`
`private boolean`	`isNavTo`
`private boolean`	`isPathGuide`
`private boolean`	`isStep`
`private int`	`iStep`
`private int`	`multiplier`
`private javajs.util.Lst<java.lang.Object[]>`	`navigationList`
`private int`	`nHits`
`private javajs.util.P3[]`	`pointGuides`
`private javajs.util.P3[]`	`points`
`private TransformManager`	`tm`
`private int`	`totalSteps`
`private float`	`xTrans`
`private float`	`xTransDelta`
`private float`	`xTransStart`
`private float`	`yTrans`
`private float`	`yTransDelta`
`private float`	`yTransStart`

Fields inherited from class org.jmol.thread.JmolThread
CHECK1, CHECK2, CHECK3, currentTime, eval, FINISH, haveReference, hoverEnabled, INIT, isJS, isReset, lastRepaintTime, MAIN, name, sc, sleepTime, startTime, stopped, targetTime, vwr

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor Description

Navigator()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`alignZX(javajs.util.P3 pt0, javajs.util.P3 pt1, javajs.util.P3 ptVectorWing)`	brings pt0-pt1 vector to [0 0 -1], then rotates about [0 0 1] until ptVectorWing is in xz plane
`private void`	`calcNavigationDepthPercent()`
`void`	`calcNavigationPoint()`
`private void`	`calcNavSlabAndDepthValues()`
`private void`	`doNavStep(int iStep)`
`private float`	`getNavigationSlabOffsetPercent()`
`java.lang.String`	`getNavigationState()`
`void`	`navigate(float seconds, javajs.util.P3[][] pathGuide, javajs.util.P3[] path, float[] theta, int indexStart, int indexEnd)`
`void`	`navigateAxis(javajs.util.V3 rotAxis, float degrees)`
`void`	`navigateKey(int keyCode, int modifiers)`
`void`	`navigateList(JmolScriptEvaluator eval, javajs.util.Lst<java.lang.Object[]> list)`
`void`	`navigateTo(float seconds, javajs.util.V3 axis, float degrees, javajs.util.P3 center, float depthPercent, float xTrans, float yTrans)`
`void`	`navTranslatePercentOrTo(float seconds, float x, float y)`
`private void`	`newNavigationCenter()`	We do not want the fixed navigation offset to change, but we need a new model-based equivalent position.
`private void`	`nextList(int i, javajs.util.P3 ptTemp)`
`protected void`	`oops(java.lang.Exception e)`
`protected void`	`run1(int mode)`
`void`	`set(TransformManager tm, Viewer vwr)`
`void`	`setNavigationDepthPercent(float percent)`
`void`	`setNavigationOffsetRelative()`
`private void`	`setNavPercent(javajs.util.P3 pt1)`
`private void`	`setupNav(float seconds, javajs.util.P3[][] pathGuide, javajs.util.P3[] path, int indexStart, int indexEnd)`
`private void`	`setupNavTo()`
`void`	`zoomByFactor(float factor, int x, int y)`

Methods inherited from class org.jmol.thread.JmolThread
checkInterrupted, interrupt, reset, resumeEval, run, runSleep, setEval, setManager, setViewer, start

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.jmol.api.JmolNavigatorInterface
interrupt

Methods inherited from interface java.lang.Runnable
run

Field Detail

tm
```
private TransformManager tm
```

nHits
```
private int nHits
```

multiplier
```
private int multiplier
```

isPathGuide
```
private boolean isPathGuide
```

points
```
private javajs.util.P3[] points
```

pointGuides
```
private javajs.util.P3[] pointGuides
```

frameTimeMillis
```
private int frameTimeMillis
```

floatSecondsTotal
```
private float floatSecondsTotal
```

axis
```
private javajs.util.V3 axis
```

degrees
```
private float degrees
```

center
```
private javajs.util.P3 center
```

depthPercent
```
private float depthPercent
```

xTrans
```
private float xTrans
```

yTrans
```
private float yTrans
```

depthStart
```
private float depthStart
```

depthDelta
```
private float depthDelta
```

xTransStart
```
private float xTransStart
```

xTransDelta
```
private float xTransDelta
```

yTransStart
```
private float yTransStart
```

yTransDelta
```
private float yTransDelta
```

degreeStep
```
private float degreeStep
```

centerStart
```
private javajs.util.P3 centerStart
```

totalSteps
```
private int totalSteps
```

aaStepCenter
```
private javajs.util.V3 aaStepCenter
```

isNavTo
```
private boolean isNavTo
```

iStep
```
private int iStep
```

navigationList

private javajs.util.Lst<java.lang.Object[]> navigationList

iList
```
private int iList
```

isStep
```
private boolean isStep
```

Constructor Detail
- Navigator
```
public Navigator()
```

Method Detail

set

public void set(TransformManager tm,
                Viewer vwr)

Specified by:: set in interface JmolNavigatorInterface

navigateList

public void navigateList(JmolScriptEvaluator eval,
                         javajs.util.Lst<java.lang.Object[]> list)

Specified by:: navigateList in interface JmolNavigatorInterface

nextList

private void nextList(int i,
                      javajs.util.P3 ptTemp)

setNavPercent

private void setNavPercent(javajs.util.P3 pt1)

navigateTo

public void navigateTo(float seconds,
                       javajs.util.V3 axis,
                       float degrees,
                       javajs.util.P3 center,
                       float depthPercent,
                       float xTrans,
                       float yTrans)

Specified by:: navigateTo in interface JmolNavigatorInterface

navigate

public void navigate(float seconds,
                     javajs.util.P3[][] pathGuide,
                     javajs.util.P3[] path,
                     float[] theta,
                     int indexStart,
                     int indexEnd)

Specified by:: navigate in interface JmolNavigatorInterface

run1

protected void run1(int mode)
             throws java.lang.InterruptedException

Specified by:: run1 in class JmolThread
Throws:: java.lang.InterruptedException

doNavStep
```
private void doNavStep(int iStep)
```

setupNavTo
```
private void setupNavTo()
```

setupNav

private void setupNav(float seconds,
                      javajs.util.P3[][] pathGuide,
                      javajs.util.P3[] path,
                      int indexStart,
                      int indexEnd)

alignZX

private void alignZX(javajs.util.P3 pt0,
                     javajs.util.P3 pt1,
                     javajs.util.P3 ptVectorWing)

brings pt0-pt1 vector to [0 0 -1], then rotates about [0 0 1] until ptVectorWing is in xz plane

Parameters:: pt0 -; pt1 -; ptVectorWing -

zoomByFactor

public void zoomByFactor(float factor,
                         int x,
                         int y)

Specified by:: zoomByFactor in interface JmolNavigatorInterface

calcNavigationPoint
```
public void calcNavigationPoint()
```
Specified by:

calcNavigationPoint in interface JmolNavigatorInterface

calcNavSlabAndDepthValues

private void calcNavSlabAndDepthValues()

newNavigationCenter
```
private void newNavigationCenter()
```
We do not want the fixed navigation offset to change, but we need a new model-based equivalent position. The fixed rotation center is at a fixed offset as well. This means that the navigationCenter must be recalculated based on its former offset in the new context. We have two points, N(navigation) and R(rotation). We know where they ARE: fixedNavigationOffset and fixedRotationOffset. From these we must derive navigationCenter.

setNavigationOffsetRelative
```
public void setNavigationOffsetRelative()
```
Specified by:

setNavigationOffsetRelative in interface JmolNavigatorInterface

navigateKey

public void navigateKey(int keyCode,
                        int modifiers)

Specified by:: navigateKey in interface JmolNavigatorInterface

setNavigationDepthPercent
```
public void setNavigationDepthPercent(float percent)
```
Specified by:

setNavigationDepthPercent in interface JmolNavigatorInterface

calcNavigationDepthPercent

private void calcNavigationDepthPercent()

getNavigationState
```
public java.lang.String getNavigationState()
```
Specified by:

getNavigationState in interface JmolNavigatorInterface

getNavigationSlabOffsetPercent

private float getNavigationSlabOffsetPercent()

navigateAxis

public void navigateAxis(javajs.util.V3 rotAxis,
                         float degrees)

Specified by:: navigateAxis in interface JmolNavigatorInterface

navTranslatePercentOrTo

public void navTranslatePercentOrTo(float seconds,
                                    float x,
                                    float y)

Specified by:: navTranslatePercentOrTo in interface JmolNavigatorInterface

oops

protected void oops(java.lang.Exception e)

Overrides:: oops in class JmolThread

Class Navigator

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class org.jmol.thread.JmolThread

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class org.jmol.thread.JmolThread

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Methods inherited from interface org.jmol.api.JmolNavigatorInterface

Methods inherited from interface java.lang.Runnable

Field Detail

tm

nHits

multiplier

isPathGuide

points

pointGuides

frameTimeMillis

floatSecondsTotal

axis

degrees

center

depthPercent

xTrans

yTrans

depthStart

depthDelta

xTransStart

xTransDelta

yTransStart

yTransDelta

degreeStep

centerStart

totalSteps

aaStepCenter

isNavTo

iStep

navigationList

iList

isStep

Constructor Detail

Navigator

Method Detail

set

navigateList

nextList

setNavPercent

navigateTo

navigate

run1

doNavStep

setupNavTo

setupNav

alignZX

zoomByFactor

calcNavigationPoint

calcNavSlabAndDepthValues

newNavigationCenter

setNavigationOffsetRelative

navigateKey

setNavigationDepthPercent

calcNavigationDepthPercent

getNavigationState

getNavigationSlabOffsetPercent

navigateAxis

navTranslatePercentOrTo

oops